A Comparison of Phenylpropanoid Pathway Gene Families in Common Bean. Focus on P450 and C4H Genes

Abstract

The focus of this chapter is on gene families encoding enzymes of phenylpropanoid pathway in common bean. The introductory section contains a short overview of the phenylpropanoid pathway. Section 11.2 introduces major gene families encoding enzymes of this pathway in common bean, soybean, and Arabidopsis in the current annotations of their complete genome sequences (Phaseolus vulgaris v1.0, Glycine max Wm82.a2.v1, and Arabidopsis thaliana TAIR10) deposited in Phytozome 10.2. For each of the 21 enzyme classes, their functional annotations were based on the commonly used Pfam and KOG databases, while the number of genes in each family was based on Phytozome and KEGG databases. Section 11.3 describes cytochrome P450s involved in the phenylpropanoid pathway with particular emphasis on ten families included in the general (central) phenylpropanoid pathway, C4H (family CYP73A), in the lignin/lignan branch, C3H (family CYP98A) and F5H (family CYP84A), in the flavonoid/anthocyanin/proanthocyanidin branch, F3′H (family CYP75B), F3′5′H (family CYP75A), and FNS (family CYP93B), and in the isoflavonoid branch IFS (family CYP93C), I2′H (family CYP81E), F6H (family CYP71D), and D6aH (family CYP93A). The availability of the complete genome sequences enabled a thorough inventory of putative P450 genes encoding enzymes of this metabolic pathway. The P450 gene sequences from common bean were compared to homologs from Arabidopsis and soybean and confirmed with the information published for both soybean and common bean genomes. Cinnamate 4-hydroxylase (C4H) is the first P450 enzyme in the phenylpropanoid pathway and is described in detail in Sect. 11.4. It belongs to the relatively small CYP73A gene family. Genome locations and gene structures including cis-regulatory regions in 5′UTRs (5′ regulatory sequences) are detailed for this family in common bean. In addition, the expression patterns of these genes in different tissues (Phytozome 10.2) and syntenic relationships (Plant Genome Duplication Database) between common bean and soybean were examined. Finally, genes encoding the C4H enzyme in landrace G19833 (Andean gene pool, Phytozome 10.2) and in cultivar OAC Rex (Mesoamerican gene pool) were compared and searched for polymorphisms. These sequence differences can be used to develop C4H gene-based marker(s) to explore the roles of these genes in various processes such as lignin or anthocyanin biosynthesis.